title: RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.
abstract: Enzymes carrying NlpC/p60 domains, for instance RipA and RipB from Mycobacterium tuberculosis, are bacterial peptidoglycan hydrolases that cleave the peptide stems and contribute to cell wall remodelling during cell division. A member of this protein family, RipD (Rv1566c) from M. tuberculosis described in the present study, displays sequence alterations in the NlpC/p60 catalytic triad and carries a pentapeptide repeat at its C-terminus. Bioinformatics analysis revealed RipD-like proteins in eleven mycobacterial genomes, whereas similar pentapeptide repeats occur in cell-wall-localized bacterial proteins and in a mycobacteriophage. In contrast with previously known members of the NlpC/p60 family, RipD does not show peptidoglycan hydrolase activity, which is consistent with the sequence alterations at the catalytic site. A strong interaction of the catalytically inactive core domain with peptidoglycan is however retained, presenting the first example of the NlpC/p60 domains that evolved to a non-catalytic peptidoglycan-binding function. Full-length RipD carrying the C-terminal repeat shows, however, a decrease in binding affinity to peptidoglycan, suggesting that the C-terminal tail modulates the interaction with bacterial cell wall components. The pentapeptide repeat at the C-terminus does not adopt a defined secondary structure in solution which is in accordance with results from the 1.17 Å (1 Å=0.1 nm) crystal structure of the protein carrying two repeat units.
authors.affiliation: *Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.
authors.forename: Dominic
authors.initials: D
authors.lastname: Böth
authors.forename: Eva Maria
authors.initials: EM
authors.lastname: Steiner
authors.forename: Atsushi
authors.initials: A
authors.lastname: Izumi
authors.forename: Gunter
authors.initials: G
authors.lastname: Schneider
authors.forename: Robert
authors.initials: R
authors.lastname: Schnell
mesh_terms: D000220:Adaptation, Biological / Q000502:physiology*; D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002384:Catalysis; D002473:Cell Wall / Q000378:metabolism; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D009238:N-Acetylmuramoyl-L-alanine Amidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D010457:Peptidoglycan / Q000378:metabolism*; D011485:Protein Binding / Q000502:physiology; D054730:Protein Interaction Domains and Motifs / Q000502:physiology*; D017386:Sequence Homology, Amino Acid
chemical_list: D000942:Antigens, Bacterial; D010457:Peptidoglycan; C072681:Mycobacterium tuberculosis antigens; D009238:N-Acetylmuramoyl-L-alanine Amidase